Bovine paratuberculosis, also called Johne's disease, is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP). Infected cattle develop diarrhea resulting in reduced milk production, severe emaciation and substantial financial losses to the farming industry. Not only cattle are receptive, but also most other domestic and wild ruminant species, making Johne's disease a growing issue to face the agricultural industry.
To date, no effective therapeutic nor vaccine agent is available, and early detection along with good management practices are the only ways to control paratuberculosis.
Most of the diagnostic tests available are limited by their relative lack of sensitivity and/or specificity.
For example, cultivation of bacteria excreted by animals at the clinical stage is highly specific, but only applicable to the latest stage of infection. Moreover, the slow growth of MAP translates into a 3-month waiting time to define individual infection status. Additionally, bacteria's shedding is clearly an inconstant phenomenon in this disease.
PCR detection of MAP on feces is rapid, but also applicable only to the late stage of infection, when animals start shedding bacteria.
Cell-mediated immunity (CMI) and serological assays remain the most promising ones, but so far remain hampered by the lack of specific immunodominant antigens.
Several antibody detection ELISA kits are commercially available, and are claimed to be highly specific. Most of them use crude cellular extracts and are based on preadsorption of the test sera on Mycobacterium phlei, to limit cross-reactivity due to sensitisation to environmental mycobacteria. However, this preadsorption step is responsible for a considerable decrease in sensitivity, particularly among animals shedding low numbers of bacilli. Moreover, it is not specified whether these tests are able to discriminate paratuberculosis from bovine tuberculosis caused by M. bovis. 
Genomic screening of the fully sequenced MAP genome has allowed to identify prospectively MAP-specific immune targets. Antigenicity of these proteins has been evaluated by Western blot using sera from a small number of cattle naturally infected with MAP. To date, a number of antigens have been identified using this genomic approach but data about their reactivity in ELISA using larger panels of sera are still lacking.
MAP specific vaccines currently available in some countries are composed of whole bacteria (killed or attenuated) formulated in mineral oil adjuvants. These vaccines confer a partial protection against MAP, reducing the levels of excretion of bacteria in feces and the productivity losses.
However, these vaccines do not protect against the infection and moreover, they interfere with the skin test used in the official control programs for bovine tuberculosis, and with the indirect diagnostic tests for paratuberculosis (antibody ELISA and IFN-γ assay).
They can also induce an undesirable, granulomatous reaction at the injection site and finally their use is not without danger for the veterinary practitioner.